Fish in the Bay – January 2021, part 1: Winter Fishes = Longfin, Shad, Herring, & Anchovy(?).

Trawl map.

Good news first: 

  • 1126 Anchovies! That is the biggest January catch of Anchovies since 2014. 
  • 465 Longfin Smelt were caught in January! That is the most ever caught in several years of regular weekend trawling here.
  • Lots of Shad: 171 American Shad and 40 Threadfin Shad.  The Shad haul was not record-breaking, but it was a decent haul.
  • One Herring! We caught one Pacific Herring during regular January trawls, but three more were netted during supplemental Longfin work as discussed further below.

But, this is the complicated part:

  • The cold is driving them in. Longfin Smelt, Shad, Herring, and Crangon Shrimp are triggered by low temperatures to migrate upstream for their spawning migrations.
  • But, lack of rain threatens the survival of fry. Populations of all these species swell during, or after, wet years as a result of successful recruitment.  No rain = poor recruitment. 

Anchovies are an outlier.  Their populations in Lower South Bay increase during drought years and shrink when it is wetter.  And, they tend to like the summer warmth: summer trawls generally catch more of them.   Most of the 1,000+ Anchovies counted this month consist of young recruits from the recent summer thru late-fall spawn.  But, we continue to see large blue adults that must be arriving from the ocean.  The Anchovy situation continues to be a confusing mystery.


Bay-side stations trawling results.


Upstream of Railroad Bridge.

La Nina = Cold dry winter.  On paper, it looks like temperatures at all stations are only a few tenths of a degree cooler than last year.  But, I suspect it has been more consistently cooler this winter. It is definitely drier and at least a few ppt saltier at all stations compared to January 2020.

According to the big ENSO index, we have been experiencing a strong La Nina (cool Sea Surface Temperatures (SST)) far out in the equatorial Pacific:

La Nina usually results in:


1. Crispy Marsh. No rain in sight. 

(Editor’s note – An Atmospheric River dumped 2 inches of rain from on 28-29 January.  This was very welcome, but not enough to turn this La Nina drought around though!

The view of Artesian Slough at launch time on Sunday 10 January: Crispy marsh!

California bulrush dominates Artesian Slough.  The bulrush is the tall tule that Native Americans used to make reed boats and shelters back in the day. 

Taller marsh plants dominate the scene in fresher water.  This is the plant order, from freshest to salty:  Cattail, California bulrush, Alkali bulrush, Pickleweed, then Spartina. 

  • Cattails require totally fresh creek water that is usually farther upstream than we can trawl. We see a few clusters of Cattails at the upstream ends of our trawls, but they usually die by late summer.
  • California bulrush tolerates a range of salinity from fresh to slightly brackish (single digit ppt). The big established colonies upstream in Alviso Slough, and from Artesian Slough through Pond A19, can withstand months of higher salinity.  But, where salinity is consistently higher the marsh transitions to …
  • Alkali bulrush, which is a shorter cousin to the California variety. Most of Alviso Slough, the main stem of Lower Coyote Creek, and Pond A21 are covered in Alkali bulrush. 
  • Spartina and Pickleweed grow in the highest salinities. Spartina grows below the lower waterline, and pickleweed at, and just above, the waterline.  (Pickleweed does not like to be submerged for extended periods whereas Spartina is adapted for that.) 

The photo above shows what acres of California bulrush looks when we get no winter rain:  dry and crispy.  These dense colonies will survive and green-up when rain returns, but downstream patches on the California bulrush frontier are doomed this year.

Reardon (1996) gives a good literature review of salt marsh plant knowledge in addition to a rigorous early-1996 survey of marsh plants in Artesian slough:


2. Longfin Smelt.

Crispy California bulrush in Pond A19 and some of the Longfins and Anchovies caught here.

Both Longfin Smelt and Northern Anchovies spawn and/or recruit in this year’s crispy marshes. Restored ponds A19 and A21 are providing a substantial portion of the desired habitat.

California bulrush continues to dominate the east side of Pond A19 indicating that water is fresher here on average. This eastern corner of A19 is a consistent fish spawning & rearing hotspot.  (The western side of the pond is at lower elevation and is covered in Spartina and mudflat.)    


Crispy Alkali bulrush dominates Pond A21.  Longfins and Anchovies like it here too.

In downstream Pond A21, the vegetation is different (Alkali bulrush dominates by far) but the fish situation is similar:  both Longfin Smelt (in winter) and Anchovies (in summer) come here to spawn but possibly to a lesser degree.

I doubt that fish recognize the different bulrush species, but they certainly would respond to higher phytoplankton, copepod, and mysid production associated with fresher California bulrush marsh.  From what we see, California bulrush is a prime Longfin and Anchovy production factory in this area. 


Spawning ready Male Longfin Smelt at Art2 on Sunday 10 January.

Tall California bulrush lines the shores of Artesian, Upper Coyote, and Upper Alviso Sloughs.  Not coincidentally Longfins and Shad crowd these upstream waters in winter just as the Anchovies do each summer.


Slightly smaller (female?) Longfins at Art2. Darker bluish dorsal color indicates that some of these fish are ready to spawn!


Male Longfins!

There is a prevailing theory that adult Longfins congregate in slightly saltier downstream waters.  When ready, the Males run upstream and prepare a nest site by fanning away sediment with their elongated anal fin.  Egg-bearing females follow a short time later.  And then, I suppose, a competitive orgy is on: females lay sticky eggs on sand, gravel, or plant roots and stems, males follow closely emitting milt to fertilize the eggs.

That is more or less the way other Smelt and Salmonids spawn.    


Longfin Males in Pond A21 on 9 January. (Male at top not darkly colored, therefore possibly not spawning-ready.)

We see adult Longfins of both sexes in the Alkali marshes of Pond A21 as well.  It would be interesting to compare Longfin spawning success in the Alkali bulrush marsh of Pond A21 compared to the fresher California bulrush marsh in Pond A19.  Tides, rainfall, and competition with other species play a huge role.  I doubt that such a comparison could be accomplished with monthly trawl data alone.


3. Anchovies.

A few of the 288 young Anchovies caught at Alv2 on 9 January.

Anchovies continue to be the local oddballs:  They are a summer-time spawning marine fish that seeks freshwater marshes upstream.  But, large numbers of them also remain here in winter.  Most of these are juvenile to young adult.  They probably hatched nearby and now grow big feeding on tiny marsh bugs. 

Contrary to all the other fishes, Anchovy populations in the Alviso Marsh Complex swell in years with little or no rain.  They seem to like this current La Nina.


Young Anchovies of various ages at Art3: young juvenile to young adult.

With the exception of station LSB2 far out in the Bay, we caught Anchovies at every location.  Most were young and nearly colorless.


Young-of-year Anchovies: Gold with green crowns at Art2.

Young Anchovies in Artesian Slough display characteristic green crowns and gold lateral lines resulting from their development in fresher water.  Many seem to linger here as year-round-residents due to a never-ending freshwater food supply.  However, I would guess that Striped Bass place firm limits on growth and sustainment on this little tribe.


Mix of Anchovy colors in Artesian slough.

At the mid-point of Artesian Slough (Art2), which is perpetually fresher on average owing to the freshwater discharge from the San Jose-Santa Clara Regional Wastewater Facility, tall California bulrush grows, and Anchovies are usually golden-green to golden. 

But, once again, we found dark blue and blue-green adult interlopers.  Anchovies do not develop dark colors near freshwater!  Where did these wandering fish come from?  And, why?  There seems to be continual episodic mixing of Anchovy populations in this area.


Anchovies were similar at all stations:  mostly colorless juveniles with a few, usually larger blue adults mixed in. 


On average, Anchovies seem to be bigger and bluer in higher salinity at downstream stations, but we will have to eventually crunch some numbers to confirm this. 


A pocket of greener Anchovies resides at the east side of Pond A19 amongst the California bulrush.  Somehow, fresher water is continually seeping in here.  Is a tiny population of year-round-resident Anchovies being sustained by this fresher water supply?

I wish we could see what Anchovies looked like here 100 years ago when Carl Hubbs observed clear/brown-backs all the way out to Sausalito.


Young Anchovy with blue crown at Coy3 on 9 January.

Very young anchovies with blue crowns show up at downstream stations.  Their young age tells us that they hatched and developed nearby, but whether their color simply indicates the salinity at which they recruited or is influenced by a genetic lineage is still a guess.

Hubbs did not see blue-backed Anchovies in 1925.


4. Up the Creek without a Paddle – Until Micah saves the day.

Tragedy struck as we brought in the net at Art2 early on Sunday.  One of the net’s paddle-boards hit the cooling water coupling on our Yamaha motor.  The plastic coupler snapped.  This motor cannot run without cooling water.  So, we were stranded in a big boat over a mile downstream from the launch.


Fortunately, Micah has training and experience as a U.S. Marine Corps diesel mechanic.  After a quick inventory of all materials we had on board, he surmised that our mechanical pencil was roughly the right diameter.  Using the pencil and a pocketknife, he fabricated a replacement coupling.

Impressive skills are required to keep these trawls running:  Absent Micah’s ingenuity, we would have been stuck there for a long time waiting for a tow.  Even worse, at least half of the important January trawls would have aborted! 


5. A Rainbow of Shad Colors – and then we caught some Herring!

Brown American Shad at Art1 on 10 January.

Brown Shad.  Shad swim upstream for spawning this time of year.  They are triggered by a drop in temperature.  They seem to seek freshwater more than the other fish we see.  They turn brown where water is freshest.


Green and brown American Shad at UCoy1 on 10 January.

Salinity at UCoy1 was variable from upstream-to-downstream and from top-to-bottom.  Not surprisingly, Shad colors varied from greenish to brown.  


Blue Threadfin (at top) and American Shad at Alv3 on 9 January.

Blue Shad!  Experiments and many observations have now firmly established that Threadfin and American Shad “blue-up” in salty water. 

But, this is the bluest Threadfin Shad we have ever seen! … Until now, we have never caught a Threadfin in salinity much above 20 ppt.  This one looks like an aquamarine jewel.  How blue can this fish go?


Pacific Herring caught near the northern shore of Coyote Creek on 9 and 23 January.

Pacific Herring arrived in January.  This is the time of year that Herring swim into North Bay to lay millions of eggs.  But, they spawn in South Bay rarely, if at all.  Nonetheless, these were spawning-sized adults.  Tom Greiner, a marine biologist at California Fish and Wildlife Service, judged from the photo that the bottom Herring shown above looks like a gravid female.  

We normally don’t catch adult-sized Herring.  They are lightning-fast swimmers.  When we tossed Herring #2 back in the Bay, it looked like a bullet shooting through the water.  They have tremendous energy. 


Herring #3 and some kind of fish eggs found on 9 January.

A third, smaller Herring was caught on the 9th(This was the only Herring caught during the regular monthly trawl.  All the others were netted as by-catch during supplemental Longfin Broodstock collection.)

Mystery eggs.  A bunch of fish eggs were also found glued to a horsemussel shell in the same trawl.  Tom Greiner also advised that these golden-colored eggs could be from Herring, or Topsmelt, or Midshipman, or from some other type of fish.  Herring eggs turn clear soon after fertilization.   Can anyone else identify these eggs?


Pacific Herring #4 was caught during a Longfin Smelt Broodstock trawl on February 6th.  A salinity/color change experiment was conducted prior to releasing this fish.

Experimental results are shown above:  This Herring showed a range of color and speed of color change roughly equal to Shad.  This could mean that most, if not all, members of the Clupeidae family of Clupeiform fishes similarly change color in response to salinity.  It is a big family, encompassing all Herring, Sardines, Sprats, and Shad.   Their color-changing abilities may be one of the key adaptations that enabled them to invade estuaries and rivers from the sea starting about 90 million years ago.

Members of the Clupeidae family are also sometimes referred to as “Alosine” (or Shad-like) species, especially amongst researchers in Chesapeake Bay and along the Atlantic Coast. 

The Anchovy lineage is more distantly related, having split off 120 to 150 million years ago.  As noted many times before, Anchovy color change is much slower and differs in other ways. 


6. Deep Thoughts about Salinity-Induced Color Change in Clupeiform Fishes.

There are many more interesting observations from January trawls, but I wanted to nail down these recent Herring findings before moving on to other topics:

Clupeiform Color Hypothesis:  The range of salinity-induced dorsal colors is similar across all members of Clupeiodei.  Dorsal sides of Anchovies (Engraulidae), American Shad (Alosinae), Threadfin Shad (Dorosomatinae) and Herring (Clupeinae) all express

  • blue colors at or above 19 ppt;
  • brown or gold colors below about 14 ppt; and
  • green colors between those two thresholds.

Color changes result from alteration of orientation or spacing of guanine crystals in iridophores.  However, the mechanism of color change in distantly related Engraulidae (Anchovy family) is slightly different; as indicated by slower rate of change, weak expression of gold color at lowest salinity, and near-immediate loss of dorsal color upon death of fish.

For recent information about phylogeny of Clupeiform fishes see:

This is a bulletized summary of our Clupeiform Color discussions in previous blog posts.  It started as an Anchovy observation from 1925, then grew from there.


Confirmation of Salinity-Induced Color Change in Pacific Herring, and the other Clupeiods/Alosines, helps focus some hunches about color change in Anchovies  … and, maybe points to other important things.


7. Leopard Shark at Alv2!

Micah carefully lowers the big Leopard Shark back into the slough.

Leopard Shark.  I believe this is the biggest Leopard shark we have caught in otter trawls.  She was very fat – likely pregnant!  She was also very far upstream on Alviso Slough owing to the current saltiness. 


There is much more to discuss.  Crangon shrimp seem to be struggling, many more fish parasites encountered in January … It never ends!

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